Michel C. A. Klein

The Semantic Web: the roles of XML and RDF

XML and RDF are the current standards for establishing semantic interoperability on the Web, but XML addresses only document structure. RDF better facilitates interoperation because it provides a data model that can be extended to address sophisticated ontology representation techniques. We explain the role of ontologies in the architecture of the Semantic Web. We then briefly summarize key elements of XML and RDF, showing why using XML as a tool for semantic interoperability will be ineffective in the long run. We argue that a further representation and inference layer is needed on top of the Webs current layers, and to establish such a layer, we propose a general method for encoding ontology representation languages into RDF/RDF schema. We illustrate the extension method by applying it to Ontology Interchange Language, an ontology representation and inference language.

Ontology Evolution: Not the Same as Schema Evolution

As ontology development becomes a more ubiquitous and collaborative process, ontology versioning and evolution becomes an important area of ontology research. The many similarities between database-schema evolution and ontology evolution will allow us to build on the extensive research in schema evolution. However, there are also important differences between database schemas and ontologies. The differences stem from different usage paradigms, the presence of explicit semantics and different knowledge models. A lot of problems that existed only in theory in database research come to the forefront as practical problems in ontology evolution. These differences have important implications for the development of ontology-evolution frameworks: The traditional distinction between versioning and evolution is not applicable to ontologies. There are several dimensions along which compatibility between versions must be considered. The set of change operations for ontologies is different. We must develop automatic techniques for finding similarities and differences between versions.

OIL in a Nutshell

Currently computers are changing from single isolated devices into entry points into a worldwide network of information exchange and business transactions. Support in data, information, and knowledge exchange is becoming the key issue in current computer technology. Ontologies will play a major role in supporting information exchange processes in various areas. A prerequisite for such a role is the development of a joint standard for specifying and exchanging ontologies. The purpose of the paper is precisely concerned with this necessity. We will present OIL, which is a proposal for such a standard. It is based on existing proposals such as OKBC, XOL and RDF schema, enriching them with necessary features for expressing ontologies. The paper sketches the main ideas of OIL.

Ontology Versioning and Change Detection on the Web

To effectively use ontologies on the Web, it is essential that changes in ontologies are managed well. This paper analyzes the topic of ontology versioning in the context of the Web by looking at the characteristics of the version relation between ontologies and at the identification of online ontologies. Then, it describes the design of a web-based system that helps users to manage changes in ontologies. The system helps to keep different versions of web-based ontologies interoperable, by maintaining not only the transformations between ontologies, but also the conceptual relation between concepts in different versions. The system allows ontology engineers to compare versions of ontology and to specify these conceptual relations. For the visualization of differences, it uses an adaptable rule-based mechanism that finds and classifies changes in RDF-based ontologies.

Structure-based partitioning of large concept hierarchies

The increasing awareness of the benefits of ontologies for information processing has lead to the creation of a number of large ontologies about real-world domains. The size of these ontologies and their monolithic character cause serious problems in handling them. In other areas, e.g. software engineering, these problems are tackled by partitioning monolithic entities into sets of meaningful and mostly self-contained modules. In this paper, we suggest a similar approach for ontologies. We propose a method for automatically partitioning large ontologies into smaller modules based on the structure of the class hierarchy. We show that the structure-based method performs surprisingly well on real-world ontologies. We support this claim by experiments carried out on real-world ontologies including SUMO and the NCI cancer ontology. The results of these experiments are available online at http://swserver.cs.vu.nl/partitioning/.

Enabling knowledge representation on the Web by extending RDF schema

Recently, a widespread interest has emerged in using ontologies on the Web. Resource Description Framework Schema (RDFS) is a basic tool that enables users to define vocabulary, structure and constraints for expressing meta data about Web resources. However, it includes no provisions for formal semantics, and its expressivity is not sufficient for full-fledged ontological modeling and reasoning. In this paper, we will show how RDFS can be extended to include a more expressive knowledge representation language. That, in turn, would enrich it with the required additional expressivity and the semantics of that language. We do this by describing the ontology language Ontology Inference Layer (OIL) as an extension of RDFS. An important advantage to our approach is that it ensures maximal sharing of meta data on the Web: even partial interpretation of an OIL ontology by less semantically aware processors will yield a correct partial interpretation of the meta data. � 2002 Elsevier Science B.V. All rights reserved.

Changing virus-host interactions in the course of HIV-1 infection

Acquired immunodeficiency syndrome (AIDS) patients may present with various clinical symptoms related to severe immunodeficiency resulting from persistent infection with the human immunodeficiency virus-l (HIV-1). CD4+ T-helper (Th) cells are an important target for HIV (Klatzmann et al. 1984, Dalgleish et al. 1984, McDougal et al. 1985), and loss of these eells in relatively late stages of HIV infection is well documented and known to be predictive for progression (Meibye et al. 1986, Fahey et al. 1984). In addition to depletion of Th eells, leukocytes from AIDS patients display a variety of functional defects finally resulting in a general disturbance of immune reactivity that includes almost all leukocyte functions. At that stage, the patient is extremely susceptible to diseases related to a variety of intracellular pathogens but also has a moderately increased risk for pyogenic infections particularly with encapsulated bacteria. Moreover, in addition to Kaposis sarcomas, opportunistic neoplasia frequently develop (Fauci 1988). One feature of HIV-1 is its great variability with respect to biological properties such as syncytium inducing (SI) capacity, replication rate and cytotropism (ChengMayer et al. 1988, Asjo et al. 1986, Von Briesen et al. 1987, Evans et al. 1987, Tersmette et al. 1988). HIV-1 isolates recovered from peripheral blood mononuclear cells of asymptomatic subjects are able to grow in phytohemagglutinin (PHA)-stimulated primary blood lymphocytes (PBL) but, in contrast to isolates

The semantic web: yet another hip?

Currently, computers are changing from single, isolated devices into entry points to a worldwide network of information exchange and business transactions called the World Wide Web (WWW). For this reason, support in data, information, and knowledge exchange has become a key issue in current computer technology. The success of the WWW has made it increasingly difficult to find, access, present, and maintain the information required by a wide variety of users. In response to this problem, many new research initiatives and commercial enterprises have been set up to enrich available information with machine processable semantics. This semantic web will provide intelligent access to heterogeneous, distributed information, enabling software products (agents) to mediate between user needs and the information sources available. This paper summarizes ongoing research in the area of the semantic web, focusing especially on ontology technology.

Matching unstructured vocabularies using a background ontology

Existing ontology matching algorithms use a combination of lexical and structural correspondence between source and target ontologies. We present a realistic case-study where both types of overlap are low: matching two unstructured lists of vocabulary used to describe patients at Intensive Care Units in two different hospitals. We show that indeed existing matchers fail on our data. We then discuss the use of background knowledge in ontology matching problems. In particular, we discuss the case where the source and the target ontology are of poor semantics, such as flat lists, and where the background knowledge is of rich semantics, providing extensive descriptions of the properties of the concepts involved. We evaluate our results against a Gold Standard set of matches that we obtained from human experts.

Tracking changes during ontology evolution

As ontology development becomes a collaborative process, developers face the problem of maintaining versions of ontologies akin to maintaining versions of software code or versions of documents in large projects. Traditional versioning systems enable users to compare versions, examine changes, and accept or reject changes. However, while versioning systems usually treat software code and text documents as text files, a versioning system for ontologies must compare and present structural changes rather than changes in text representation of ontologies. In this paper, we present the PromptDiff ontology-versioning environment, which address these challenges. PromptDiff includes an efficient version-comparison algorithm that produces a structural diff between ontologies. The results are presented to the users through an intuitive user interface for analyzing the changes that enables users to view concepts and groups of concepts that were added, deleted, and moved, distinguished by their appearance and with direct access to additional information characterizing the change. The users can then act on the changes, accepting or rejecting them. We present results of a pilot user study that demonstrate the effectiveness of the tool for change management. We discuss design principles for an end-to-end ontology-versioning environment and position ontology versioning as a component in a general ontology-management framework.